Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences

Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences

^*Wellcome Trust Centre for the Epidemiology of Infectious Disease (WTCEID), University of Oxford, South Parks Road, Oxford OX1 3FY, United Kingdom; ^§Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom; ^¶Yale University School of Medicine, Department of Epidemiology and Public Health, 60 College Street, Box 208034, New Haven, CT 06520; ^‖Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom; ^**Section of Molecular Genetics, Division of Pediatric Infectious Diseases, Maxwell Finland Laboratory for Infectious Diseases, Boston University Medical School and Boston University Medical Center, Boston, MA 02118; and ^‡‡Molecular Infectious Diseases Group, University Department of Paediatrics, Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford OX3 9DS, United Kingdom

Edited by John J. Mekalanos, Harvard Medical School, Boston, MA, and approved October 23, 2000 (received for review September 5, 2000)

Abstract

The identification of clones within bacterial populations is often taken as evidence for a low rate of recombination, but the validity of this inference is rarely examined. We have used statistical tests of congruence between gene trees to examine the extent and significance of recombination in six bacterial pathogens. For Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus pyogenes, and Staphylococcus aureus, the congruence between the maximum likelihood trees reconstructed using seven house-keeping genes was in most cases no better than that between each tree and trees of random topology. The lack of congruence between gene trees in these four species, which include both naturally transformable and nontransformable species, is in three cases supported by high ratios of recombination to point mutation during clonal diversification (estimates of this parameter were not possible for Strep. pyogenes). In contrast, gene trees constructed for Hemophilus influenzae and pathogenic isolates of Escherichia coli showed a higher degree of congruence, suggesting lower rates of recombination. The impact of recombination therefore varies between bacterial species but in many species is sufficient to obliterate the phylogenetic signal in gene trees.

Footnotes

↵ † E.J.F. and E.C.H. contributed equally to this work.
↵ ‡ To whom reprint requests should be addressed. E-mail: ed.feil{at}ceid.ox.ac.uk.
This paper was submitted directly (Track II) to the PNAS office.
Data deposition: The sequences reported in this paper have been deposited in the GenBank database (accession nos. AF322666–AF322850).
Abbreviations:

SLV,

single-locus variant;

MLST,

multilocus sequence typing;

MLEE,

multilocus enzyme electrophoresis;

ML,

maximum likelihood;

r/m,

recombination/mutation